Mass Effect 3: Darker Days
by Major Swift
Summary: The Reaper war is over. With the threat behind him Shepard finally has time to settle down and relax...or does he? Someone has targeted him and his squad, with no time to lose Shepard sets out with those who remain. Who is behind it all?
1. Misleading Information

It had been four months since the war with the Reapers had ended, a war that had lasted just over a year after the Crucible had evened the field out by disabling the barriers of Reaper ships permanently; nothing interesting had really happened since then. Shepard and Tali were in his cabin on the Normandy, lying on the bed looking up at the stars through the ceiling window when the message came.

"Shepard," Joker said over the intercom, "there's a report that's just come in down here that I think you should see."

Shepard sighed; lately he had been thinking of letting Tali know about how he wanted to finally settle down with her on Rannoch. After all he had done and been through so far in his career in the Alliance and as a Specter he was ready for that kind of life. He got up and made his way to see what this report had in store for him; shooting a glance back at Tali that told her all of his feelings about this whole upcoming situation more than words could.

The door of the elevator opened to the CIC, he noticed that Traynor looked like she had something particularly distressing that she was currently dwelling on in her mind.

"Is everything alright Samantha?"

"I'll be fine…. It's just…. I'll let Joker fill you in Shepard, you'll understand."

Shepard arrived at the helm of the Normandy; Joker gave him the report without a word, just a stare of disbelief and shock. _Shepard I have some bad news for you_, the report, obviously from Hackett started off, _a couple of days ago we found out that one of your old team members who was with you mainly during your time with Cerberus, Jacob Taylor, has gone missing. We have an investigator at his house on Earth looking into things right now. He can fill you in on all of the details when you arrive, but I thought you'd want to know this; Dr. Brynn Cole was found dead in the house. Good luck Shepard, Hackett out._

After reading the report he just stood there looking at it with a frustrated and puzzled look on his face. Why would someone have done this? Where was Jacob?

"Joker, I think you know where we need to go. Set a course for Earth."

He left the room not sure of exactly how he felt one way or the other as he made his way back to his cabin to let Tali know about what had happened. Traynor gave him an understanding nod when he passed her and entered the elevator. The door opened and he walked back into the room and from the look on his face alone Tali could tell that something bad had happened.

"What happened Shepard? I can see you're upset about something." she asked, as he sat down next to her on the bed.

"I know you haven't exactly liked Jacob that much seeing as he used to be with Cerberus, but the report I just read says he's missing, that Dr. Cole was found dead in their house on Earth. I'm to go there to meet with an investigator that's been looking into it."

"Shepard, I don't know what to say," she started saying while turning to him and putting his hand in hers, " I'm sorry and I hope it turns out that Jacob is safe, I may not have liked him like you said, but he's a good man at heart. I'm coming with you when you go down to meet the investigator, it's all terrible...I just hope that we find the bosh'tet that killed Dr. Cole and find him."

"I do too Tali. And no, this is something I have to take care of on my own. I'm sorry, please understand this."

After a brief pause she looked at him and said, "It's fine, I understand. Just be careful if you find out who did it and decide to go off on your own... please."

"It's a deal then," he said as he reached over and took her mask off and kissed her.

When they arrived at Earth, Shepard went down in a shuttle alone; Cortez was with him but only to pilot the shuttle of course. He arrived at the house; the sight of a holographic police line greeted him at the door. He walked through it and found the investigator Hackett had mentioned who began to give him a rundown of what had been found so far.

"This window here near where we found Dr. Cole's body had been broken by someone as you can see. It looks like whoever killed her had jumped through it and had snapped her neck in an instant so it had to be someone trained just for things like this," they walked into the living room of the house, "a hand to hand struggle took place here and there are signs that biotics were used, more than likely from Jacob who was defending himself. Things get interesting if you take a look over here in the kitchen."

The door to the kitchen opened and on the floor were a few body bags.

"It seems the main assailant wasn't alone and whoever they were they came in numbers, more than likely more than what you see here; these are the only ones Jacob was able to kill. I've saved the best thing we found for last, it's in the basement."

They got to the basement door, the investigator insisted Shepard went down first. He opened the door, it was extremely dark and he couldn't see anything. Before he could find where the light was he was kicked in the back sending him down the stairs; his pistol landing somewhere nearby him.

"It was foolish of you to come here alone Shepard, I was expecting you to at least bring someone…..like Tali," the investigator said with a grin on his face, "I would have enjoyed putting you through that kind of pain before your end. This just makes everything easier though, and don't worry because after we're done with what we have planned for you, you'll soon be joining your friend Jacob."

Shepard started to get up as the lights flashed on. When he stood up fully he saw something on the ground in the corner; it was Jacob. He turned around to see the investigator right there behind him who then delivered a kick to his chest. Shepard slammed into the wall and lunged at him as soon as he recovered; a fist fight followed this. Whoever this guy was it was clear he had the upper hand in such a contest. He blocked a punch from Shepard while grabbing him and throwing him into the wall again; Shepard fell to the ground and saw his pistol next to him. He grabbed it and got up but unknown to him his foe had drawn a blade of sorts and stabbed him with it just as Shepard turned and shot at him. Shepard fell back into the wall as the man also fell, the bullet had found its target; his head. The blade had punctured his armor and skin by his shoulder but hadn't gone too deep. He pulled it out with a grunt of pain and threw it to the ground.

Holding his shoulder with his hand, he then walked over to the corner of the room to check Jacob; he had been stabbed multiple times and was gone. He made his way upstairs; the door to the kitchen was still open and he decided to take a look to see exactly who was in the body bags. He looked inside one and saw someone in an Alliance uniform. As he was examining the person, someone burst out from one of the other bags and began shooting at Shepard. One shot caught him in the arm as he dove out the door; he winced from the pain. He got up and fired off a couple of shots into the room as he ran out into the yard where he entered.

"Steve I need you to bring the shuttle here right now! And let Dr. Chakwas know I'm going to need to make use of her services when we get back to the Normandy." Shepard said over the comm.

Cortez arrived moments later, and with one last look at the house to see if the man was going to pursue him further, Shepard boarded the shuttle. Instead of answering questions all that had happened down there had created even more questions for him. Who were those men who had killed Jacob and Dr. Cole? What was the motive behind all of this? What did they want with him?


	2. Omega

"Hey Loco, what the hell happened down there?" James asked as the shuttle landed in the Normandy's bay and Shepard got out.

"That's what I'd like to know." Shepard replied as he started walking out of the shuttle bay. When he got to the elevator, the door opened to reveal Tali who immediately hugged him.

"I thought I told you to be careful." She said in a concerned voice.

"I tried to be. Watch the shoulder," he said with a slight groan of pain as she let go of him and saw the wounds, "that so called investigator I was suppose to meet did this. There was one other guy waiting for me there as well, shot me in the arm. I'm going to go up to the war room and speak to Hackett over the QEC and figure out just what the hell is going on."

"Shepard, the only place you need to go to right now is the med-bay. You can talk to him afterwards."

"No, this can't wait! One of my friends was killed and then used as bait to lure me there! I need to know if Hackett knows anything about what the hell just happened to me down there!" Shepard said in a harsher tone than he meant to as they both got into the elevator, "I'm sorry, I didn't mean to take a bit of this out on you. I know that you're right, I'll keep it brief with him and get down to the med-bay ASAP."

"Ok," she said reluctantly, "and you don't need to apologize. I understand how all of this must feel," she said as the door opened to the crew deck and she stepped out, "I'll wait for you there."

Shepard arrived on the main deck moments later and after going through the security field he was in the war room. He pressed a button on the QEC console and a few minutes later the blue holographic form of Hackett appeared.

"What is it Shepard?"

"Admiral what the hell is going on? I went to Earth to check with the investigator you sent to find out about Jacob's disappearance like the report I got from you said and the next moment I know I'm being attacked by him and Jacob is dead! So again I ask you sir, what the hell is this all about?"

"Calm down Shepard, what report are you even talking about? I didn't send you a report and what you said about Jacob is news to me. The only thing I've heard about lately that's happened around where he lived was that someone was concerned about something and called an Alliance patrol into the area to check things out, but we haven't heard back from them yet."

"Do you have any idea of who could have sent it then?" Shepard asked while trying to think of someone who could even remotely be responsible, "And I found that patrol in his house, they were dead."

"Damn it! And I'm sorry Shepard I don't know, but I'll start having some people look into this just in case it's someone from within the Alliance, you proceed how you see fit with this, Hackett out."

_Proceed? How? I have no idea of where to even begin. _He thought as he made his way down to the med-bay.

"You just seem to find any way you can to get injured don't you Shepard." Chakwas said when he entered the room.

"What can I say, it's a favorite hobby of mine," he said jokingly as she began to treat his wounds, "Tali, Hackett didn't know anything and he didn't send the report so I'm pretty much back to where I started with this whole thing. Can you have everyone meet up in the lounge so we can figure out where the best place to even start is? I'll be there after this and after I have talk to Joker."

"Of course Shepard." she said as she turned to leave.

Everyone had assembled in the lounge; Liara, Tali, James, Kaidan, Garrus, Javik and EDI, waiting on Shepard to arrive. Kaidan and James decided to have a drink and play a hand or two of poker while discussing the current situation; Garrus joined in as well. Javik was looking out the window, occasionally turning to say things to Liara as she talked to him while EDI and Tali chatted about things.

"So," Kaidan started saying to James, "where do you think the best place to start would be?"

"I'd say Earth but we've already been there and nothing helped so the Citadel would be my next choice," James replied, "so what do you got?"

"I was thinking of the Citadel too, but the best place to go to find out about the guys who attacked Shepard would be Omega. I'm sure some of the mercs there might have known them, maybe even Zaeed would know. I have a full house by the way," he said as he laid his cards down on the table, "How about you?"

"Shit!" James exclaimed, "All I've got is a pair of fives."

"Well that beats my straight," Garrus said as he put his cards down, "and you bring up a good point Kaidan. Omega would probably be a good place to start."

"Omega?" Shepard asked as he walked in, just catching the end of the conversation. "That seems like a good starting point, any other suggestions?"

"Unfortunately, I haven't been able to find out anything that would help us using my network yet," Liara said, "the Citadel and Illium would also be good, but I agree Omega would be best."

Everyone seemed to be in agreement with what the best choice would be.

"Omega it is. Joker," Shepard said over the comm, "Looks like we'll be heading to Omega. If you can, let Zaeed know we'll be coming to see him."

Omega, even after Cerberus's occupation and eventual departure when Shepard helped Aria take back Omega during the war with the Reapers, was still the same pisshole it always had been. The airlock door opened to the familiar sight of the station as Shepard and the squad stepped out. They walked until they got to the outside of Afterlife where they saw Zaeed examining his gun while waiting.

Zaeed looked up and upon noticing them said, "Shepard, hope you're not here just to tell me about how much you miss me."

Shepard shook his head, "No, although I wish that was the reason I was here," Shepard turned to face the squad, "Kaidan, you come with Zaeed and I. Liara, Javik and James you go to Kima District and check with any of the mercs in the area. Garrus, Tali, and EDI you go to Gozu District and do the same. Head back to the Normandy when you've finished."

They all went to carry out their assignments as Shepard, Kaidan, and Zaeed walked into Afterlife; Shepard brought Zaeed up to speed about all that had happened during the walk. They sat down at one of the bars to get drinks while they discussed things. Zaeed wasn't sure what to tell Shepard as he hadn't really heard much of anything happening on Omega or of anyone that may know of anything; save for one person.

"There is this one batarian, Farik, who could possibly know something. He's been acting odd lately, like someone hired him on for something big; I was actually going to pay the little bastard a visit soon. Owes me some credits from a bet on a mission we went on together."

After talking awhile longer and finishing their drinks they left Afterlife and headed for Farik's apartment where hopefully some answers could be found regardless of how much of a long shot it all was. They arrived there moments later; Zaeed took out a grenade and threw it towards the door.

"I see you're still doing things the subtle way Zaeed." Shepard said as the grenade exploded and the door blew open.

Zaeed walked in while Shepard and Kaidan stayed outside. A moment later Zaeed reappeared, dragging Farik in one hand. He then threw Farik out the outline of what was once a door.

"I was going to bring your credits to you today Zaeed I swear!" Farik cried out in terror while coughing on smoke from the explosion.

"This isn't about that you slippery bastard, I know someone hired you for something, what's the goddamn job?"

"What are you talking about? I haven't been hired for…."

Zaeed put his foot on his neck before he could finish his sentence, "Don't give me that, you've told that to me before any time you didn't want me along for a mission. Tell us now!"

"Ok, I'll tell you just don't kill me! I was hired by …." A couple sniper rifle shots went off hitting Farik before he could reveal anything including who had hired him and for what exactly. Another set of shots went off, one round grazing Zaeed's pauldron.

They started to run while Kaidan threw a couple of cryo blasts at their pursuers, batarians and humans by the look of it; there seemed to be a sizable number of them. From what Shepard could tell they had similar uniforms to the two men he had faced on Earth. They found a position that had some cover and stopped for a moment, ready to face the oncoming horde in the event the other teams hadn't made it back to the Normandy.

"Joker is everyone back yet?" Shepard asked over the comm.

"Everyone except for Kaidan and yourself, Commander."

"Thanks Joker," he turned to look at Zaeed, "Are you coming Zaeed?"

"I haven't ran from a fight yet and I'm not about to start now, besides, these bastards deserve to be killed. You go ahead Shepard and good luck."

Shepard put a hand on his shoulder and gave him respectful nod as the small army of people came around the corner and began to open fire; Shepard and Kaidan continued on for the Normandy.


	3. Uncertainty

Zaeed took out his assault rifle and began to pick off those who charged his position. One by one they fell, though they quickly started to take up positions with cover. Feeling a bit overconfident, Zaeed rolled out from behind his location sacrificing his protection and began to rush his opponents; breaking one's neck with a hit to the face from the butt of his rifle. One of the batarians pulled out a knife and tried to stab him with it, but he grabbed the batarian's arm, disarmed him, and then stabbed him in the neck with it all in one fluid motion. A few sniper shots went off; the world around him grew quiet. He looked down at his chest and saw three holes in his armor, blood oozing out of them. He summoned up enough energy to start moving again and took out another of his attackers; more shots went off. Zaeed stumbled and then fell on to his back, a group of batarians closed in to finish him off; one drew a pistol and pointed it at his face.

"Any last words, human?"

"Just…..this…." Zaeed said as he tried to laugh, coughing up blood in the process; a grenade in each hand.

Shepard and Kaidan could faintly hear the explosion as they boarded the Normandy. Shepard knew it deep down; another friend had been lost to this ordeal.

"Joker, get us out of here!"

The team gathered in the war room to discuss things that had been learned while on Omega; _it had better not be another dead end_ Shepard thought.

"As you are all probably aware," began Shepard, "we had a lead, but were ambushed shortly afterwards. Liara, did any of you find something useful?"

"I'm afraid not Shepard, those that did talk to us were of no help, most just brushed us off….uncivilly."

"Garrus, how about your group, did you find anything that could possibly help?"

"Well, we ran into someone interesting while we were checking around. Darner Vosque was there and after some….persuasion he told us that an old friend of ours, Balak, had been on Omega recently and had been recruiting batarians on the station for something although he didn't know what."

"That's….interesting," Shepard said while thinking of how Balak could possibly be involved, "there were humans with the batarians that were after us. Balak hates humans though; I can't see him working with them."

"Consider this Commander," Javik said joining the conversation, "someone will do whatever it takes to see something they want accomplished, especially if it's all worth it in the end in their eyes."

Shepard stopped to think for a moment, maybe it could be Balak. He could be trying to get revenge on him for all of the batarians that had lost their lives in the Bahak system when he had crashed that asteroid into the mass relay there to delay the Reapers advance.

"Well I'll admit it could be a possibility. I'd like to go to the Citadel next, at least until we have an idea of where to go," he turned to look at Liara, "While everyone else is on the Citadel I want you to stay here on the Normandy and use everything at your disposal to find out where Balak could be."

Around six months after the initial victory over the Reapers at Earth, engineers were able to get the Citadel back to where it had originally been in the Widow system. All who had survived the Reaper takeover or had escaped before it was brought to Earth had returned a month later; the Council and Commander Bailey were among those who survived. Looking around the Citadel you could never have guessed that something like that had ever happened; things had returned to normal rather quickly. Only when you went to certain places would you see the areas of the Citadel that were still under repair from both the Reaper attack and the coup attempt. Everyone went their own way once the Normandy docked in Bay D24 and Shepard decided to pay a visit to the Specter office before going to see Bailey. He checked the information terminal there for anything useful but nothing turned up which was of no surprise to him seeing as everywhere else had provided the same results so far, save for Balak's possible involvement.

"Shepard," Bailey said as Shepard walked in, "what brings you to the Citadel this time, more requests from the politicians here on the Presidium?"

"Actually I'm here on my own business this time, something more personal. I've been targeted by someone and the only lead I have as to who is Balak, a batarian that had been causing trouble here on the Citadel during the war with the Reapers and even before that with the asteroid he almost smashed into Terra Nova. Two of my squadmates have been killed, has there been anything strange going on here?"

"I'm afraid things are the same as they usually are here, politicians squabbling over things that no one should care about and petty criminals trying to get ahead in the world, nothing to get excited about."

Shepard looked at him closely, it seemed like he was trying hard to hold something back from him, "Are you sure Bailey?"

"Yeah Shepard, nothing really interesting has happened here since I got shot in the coup attempt and when the Reapers took the station. It's been a pretty boring job since the promotion."

It was more apparent than before this time, something wasn't right here, "Ok, I think I should go then Bailey."

"Wait Shepard, don't leave yet," Bailey said as Shepard started to walk towards the door, "maybe you should stay and look around awhile, maybe you'll find something, if nothing else maybe we could get a drink at that bar in Purgatory."

Shepard turned around and walked back up to Bailey's desk, "But you just said that nothing out of the ordinary is happening here. It was nice to see you again Bailey but I've got to go."

Bailey sighed; he appeared to be in pain as if fighting something. He then said as Shepard turned to walk out, "I didn't want to have to do it this way," the sound of a pistol being drawn echoed in the room, "I'm sorry Shepard but I can't let you leave."

Shepard turned around to see Bailey pointing a pistol at him and walking towards him. The door to his office opened and three C-Sec agents walked in.

"Bailey, what the hell is going on?

"I'm sorry Shepard," he said again and then looked towards the agents, "take him away, you know who to bring him to."

Just as they began to move Shepard knocked the pistol out of Bailey's hand and punched him in the face sending him stumbling back over his desk. He then turned to face the three agents, one lunged at him with a punch and Shepard grabbed his arm, put it into a joint lock, broke it and then threw him into the wall. One of the other agents slammed Shepard into the wall a second later and then hit him in the chest. He went to hit Shepard again, this time in the face but Shepard ducked, whirled around him, elbowed him in the stomach and kicked the back of his knee to drop him to the ground. He turned to face the third one and was immediately pistol whipped across the face by Bailey; sending him to the ground dazed.

"Restrain him and get him out of here!" Bailey said with a look of regret on his face.


	4. Loss

The two agents got him to his feet; the third watched from afar holding his arm with a look of extreme pain on his face. A moment later the doors to the office opened and the agents were hit with biotic throws; Shepard fell to the floor, still dazed from being hit with the pistol. Bailey and the third agent had only a second to react before they themselves were hit with a biotic slam leaving them unconscious on the ground. As he was being helped up he realized who it was.

"Liara, what are you doing here? I thought I told you to stay on the Normandy."

"I don't think now is the best time Shepard, let's get out of here first just in case more of them show up."

They left the office and started making their way to the Normandy, attempting to avoid any C-Sec officers they came across along the way.

"What about the rest of the squad?" Shepard asked while they were hiding around a corner waiting for the C-Sec patrol to leave that had just entered the area.

"I already warned them and hopefully by now they are back on the Normandy, I couldn't get through to you so I feared I was already too late so I came to get you but I'll tell you more once we're back."

The patrol seemed to receive a message via radio; they then drew their weapons and started to run towards the direction of the elevator Shepard and Liara had just gotten off. It seemed they were on to them now if they hadn't been already and were likely heading to the area around Bailey's office; luckily bay D24 was just a short distance away. They got near the door to the bay and saw that a C-Sec officer was standing watch over it. Shepard started to slowly move towards the officer while his back was turned while Liara followed closely. He went to grab hold of him when suddenly the officer just disappeared; it had been a decoy.

They heard a laugh and turned around to see the real officer had been behind them watching the entire time.

"I've already told the others you're here," said the officer with a smug look on his face, "might as well just give up now and save yourselves some…"

Before he could finish Liara hit him with her biotics sending him flying backwards into the wall at the far end of the room. They ran the rest of the way to the Normandy knowing that there wasn't much time left.

"Joker, get us out of here now!" Shepard yelled as they boarded the Normandy.

"I can't Commander, the controls are locked out."

"One moment," said EDI as she began to work on getting them unlocked, "there I've overridden it."

"Commander, Kaidan is still out there," said James, "we were heading back but had to split up when we saw some C-Sec heading our way, I was the first one back and he still hasn't showed up."

"Damn it," Shepard said, the frustration in his voice clear, "We can't leave him here."

He went back to the airlock door but as it opened he saw that a lot of C-Sec had shown up and Kaidan was currently trying to fight his way through the horde as best as he could to get to them. One of them got close to him and hit him in the back of the head with a pistol, dropping him to the ground. They then began to drag him out of the bay; Shepard, along with James and Liara opened fire on them but their numbers were too great.

"Shepard, we have to go!" Liara shouted as she put up a bubble of biotic energy to shield them from the oncoming fire from C-Sec.

"No, we can't leave him!"

James grabbed Shepard and started to pull him back inside the Normandy knowing that if they stayed any longer C-Sec would eventually overwhelm them and they'd all end up being taken like Kaidan.

"Let go James!" Shepard said struggling to get back to the fight while Liara moved back into the ship with them.

They got inside and James told Joker to leave while Liara tried to say something to Shepard but he just turned and walked away, heading to the elevator to go to his cabin.

"I don't know how much more he can take," James said turning from Joker to face Liara.

"He's been through more than most would care to, both physically and mentally."

"I'll say," James replied, "I still remember that crazy stunt he pulled back on Noveria when we were fighting the Reapers and we almost lost Tali when she got cut off from the rest of us and he went through that entire horde to get to her. I've never seen anyone fight like that before, well besides a krogan anyway."

Around twenty minutes had passed and Shepard was still in his cabin. Most of the squad decided to give him some time alone so Liara held off on trying to tell him the information she had discovered. James thought differently though and figured there was one person on board that Shepard would want to talk with.

"Sparks." James said as he entered Engineering, nearly walking into Tali who was heading to the door.

"Why must you insist on calling me that?"

"It's just what I do; anyway I think you should go talk to Shepard, all of this has been pretty rough."

"I was just going up to see him now, has Liara told him what she found out yet?"

James shook his head, "She's still waiting."

"Shepard," Tali said as she entered his cabin and sat down on the bed next to where he was laying, "we'll get him back."

"I just…..it's… it's frustrating when I all I can do is watch these things happen, being able to do absolutely nothing to prevent any of it from happening. If I had done better then…."

Tali cut him off before he could finish his sentence, "You did the best you could and more, everyone knows that."

"Well maybe my best just won't be enough against whoever is doing this."

Tali figured she should change the subject, "Do you miss the house Shepard? We only got to stay in it a couple of weeks before the Alliance called you back to the Normandy but I miss it a lot."

"Yeah I do Tali, I miss the porch in the back that looks out over the water, I miss all of those breathtaking views on Rannoch, I even miss that damn shed I couldn't seem to build and am still trying to build."

Tali laughed, "I don't think carpentry is one of your talents," she said teasingly, "it's good that the geth are there to help otherwise we wouldn't have accomplished as much as we have. I think you should ask one of them to help when we get back."

"Never, I'll build that thing if it's the last thing I do," He said smiling, "We'd already be back if all of this hadn't started happening, I was ready to leave the Alliance and get back there."

Shepard sat up and they hugged and then Tali said, "Well then, the sooner this is over then the sooner we can go home. As you already know Liara found some information that could be useful."

Shepard paused for a moment then said over the comm to Joker, "Joker, have everyone meet in the war room, I'll be there shortly."


End file.
